Chlorine in PDB 5vrz: Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 60 S

All present enzymatic activity of Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 60 S:
2.7.7.7;

The structure of Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 60 S, PDB code: 5vrz was solved by A.J.Reed, Z.Suo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.83 / 2.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.700, 79.800, 55.300, 90.00, 107.20, 90.00
R / Rfree (%)	19.7 / 24.2

The structure of Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 60 S also contains other interesting chemical elements:

Magnesium	(Mg)	5 atoms
Sodium	(Na)	1 atom

The binding sites of Chlorine atom in the Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 60 S (pdb code 5vrz). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 60 S, PDB code: 5vrz:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 60 S


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 60 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:43.7 occ:1.00 O T:HOH115 2.8 33.8 1.0 N6 T:DA6 3.1 20.5 1.0 ND2 A:ASN37 3.4 32.2 1.0 OD1 A:ASN37 3.4 35.0 1.0 CG A:ASN37 3.8 32.6 1.0 NH1 A:ARG40 3.8 42.5 1.0 NZ A:LYS280 3.8 37.2 1.0 CE A:LYS280 3.9 33.6 1.0 O P:HOH520 3.9 35.8 1.0 CD A:LYS280 3.9 29.2 1.0 O P:HOH509 3.9 44.5 1.0 N7 T:DA6 4.0 23.1 1.0 O T:HOH104 4.1 52.8 1.0 C6 T:DA6 4.1 21.2 1.0 CE2 A:TYR36 4.4 31.5 1.0 C5 T:DA6 4.4 22.7 1.0 O4 P:DT11 4.7 20.7 0.8 CG A:LYS280 4.9 27.6 1.0 CD2 A:TYR36 4.9 30.1 1.0 CZ A:ARG40 4.9 41.5 1.0 O6 T:8OG7 4.9 22.2 1.0 O4 P:TTP101 5.0 12.6 0.2 CD1 A:ILE33 5.0 41.4 1.0

Chlorine binding site 2 out of 2 in the Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 60 S


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Human Dna Polymerase Beta 8-Oxog:Dc Extension with Dttp After 60 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl402 b:34.9 occ:1.00 ND2 A:ASN294 3.2 18.2 1.0 O A:HOH655 3.2 41.6 1.0 O A:HOH646 3.2 38.7 1.0 OG1 A:THR297 3.2 23.8 1.0 OD1 A:ASN294 3.9 19.9 1.0 CB A:TYR296 3.9 21.7 1.0 NH1 A:ARG299 3.9 41.5 1.0 CG A:ASN294 3.9 18.9 1.0 CZ A:ARG299 4.0 38.8 1.0 CG2 A:THR297 4.0 23.9 1.0 CD2 A:TYR296 4.0 23.5 1.0 CB A:THR297 4.2 23.8 1.0 NE A:ARG299 4.3 34.3 1.0 NH2 A:ARG299 4.3 36.2 1.0 CG A:TYR296 4.4 22.4 1.0 CD A:ARG299 4.6 33.0 1.0 O A:HOH607 4.6 25.7 1.0 N A:THR297 4.7 22.3 1.0

A.J.Reed, Z.Suo. Time-Dependent Extension From An 8-Oxoguanine Lesion By Human Dna Polymerase Beta. J. Am. Chem. Soc. V. 139 9684 2017.
ISSN: ESSN 1520-5126
PubMed: 28682600
DOI: 10.1021/JACS.7B05048